Initial commit

.gitignore

@@ -0,0 +1,8 @@
+/*
+!.gitignore
+!*.md
+!*.sh
+!error*.log
+!contrasts.tsv
+!*.py
+

README.md

@@ -0,0 +1,46 @@
+# HW7: First level analysis
+
+Due 4/19.
+
+
+## Part 1: Finish in-class exercise
+
+Complete the level 1 and level 2 analysis we started in class on 4/13. You do not need to submit anything, but you will need the level 2 outputs for all subjects for the 4/20 class meeting.
+
+## Part 2: Level 1 analysis on your data
+
+1. Fork and clone this repository to the cluster. You will also want to clone the [volume](https://github.uconn.edu/psyc5171/volume_scripts) or [surface](https://github.uconn.edu/psyc5171/surface_scripts) repository that contains the processing scripts we discussed in class.
+2. Edit `contrasts.tsv` to specify your first level contrasts of interests. These contrasts will compare different conditions within a single run of the task. If your analysis plan includes comparisons between different tasks/sessions/subjects, those will be calculated at the group level.
+3. Edit `sbatch_level1.sh` to specify a level1 processing job for a specified subject/session/task/run.
+4. Use the `sbatch` command to submit one run of your `sbatch_level1.sh` script and make sure it works.
+4. Edit `submit_level1.sh` to use a loop to submit a level1 job for each run you need to analyze. You will need to pay careful attention to the paths in the script. This script will be run at the command line on the cluster, so the paths need to be specified with respect to the filesystem on the cluster, as opposed to a filesystem in a container.
+5. Run your `submit_level1.sh` script to queue all the level 1 analyses.
+5. Edit `sbatch_level2.sh` to specify a second level processing job that averages across runs. You can use this even if your data does not have multiple runs.
+6. Once your level 1 analyses have completed, use the `sbatch` command to submit one run of your `sbatch_level2.sh` script and make sure it works.
+7. Edit `submit_level2.sh` to use a loop to submit a level2 job for each subject/session/task you need to analyze. You will need to pay careful attention to the paths in the script. This script will be run at the command line on the cluster, so the paths need to be specified with respect to the filesystem on the cluster, as opposed to a filesystem in a container.
+8. Run your `submit_level2.sh` script to queue all the level 2 analyses.
+
+### Submission
+
+- Use git to add, commit, push
+- [Create a pull request](https://github.uconn.edu/psyc5171/hw7)
+
+
+## git workarounds
+
+- To associate your clone with your GitHub username, run the command
+
+	```bash
+	git remote set-url origin \
+	https://${USER}@github.uconn.edu/${USER}/hw7.git
+	```
+	in your `hw7` directory. This will avoid the `The requested URL 	returned error: 403 Forbidden while accessing ` error when pushing.
+- Use the command `unset SSH_ASKPASS` prior to pushing to avoid the error `(gnome-ssh-askpass:19484): Gtk-WARNING **: cannot open display:`
+- When committing, you can specify a short commit message on the command line with the `-m` option: `git commit -m 'commit message'`. If you do not do this, the default editor will open so you can write your commit message. The default is usually `vi`.
+	- Press `i` to enter insertion mode and write your message
+	- Press `ctrl-c` or `esc` to exit insertion mode
+	- Type `:wq` to save and quit or `:q!` to quite without saving
+
+- The command `git status` will show files that have changed since the last commit.
+- The command `git log` will show the commit history
+

sbatch_level1.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=First.Last@uconn.edu
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=2gb
+#SBATCH --time=00:15:00
+#SBATCH -e error_%A_%a.log
+#SBATCH -o output_%A_%a.log
+#SBATCH --job-name=level1
+#SBATCH --partition=general
+
+participant=$1
+run=$2
+
+module load singularity
+singularity run --cleanenv \
+    --bind /your/directory:/data \
+    /scratch/psyc5171/containers/nipype.sif \
+
+

sbatch_level2.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=First.Last@uconn.edu
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=2gb
+#SBATCH --time=00:15:00
+#SBATCH -e error_%A_%a.log
+#SBATCH -o output_%A_%a.log
+#SBATCH --job-name=level2
+#SBATCH --partition=general
+
+participant=$1
+
+module load singularity
+singularity run --cleanenv \
+    --bind /your/directory:/data \
+    /scratch/psyc5171/containers/nipype.sif \
+

submit_level1.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+cat bids/participants.tsv | tail -n +2 \
+| awk '{print $1}' | sed -e 's/sub-//' \
+| while read sub; do
+	for run in `seq -f '%02g' 2`; do
+		sbatch sbatch_level1.sh $sub $run
+	done
+done
+

submit_level2.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+cat bids/participants.tsv | tail -n +2 \
+| awk '{print $1}' | sed -e 's/sub-//' \
+| while read sub; do
+	sbatch sbatch_level2.sh $sub 
+done